Abstract 2083: Solving the problem of spatial informatics: Harnessing the power of the cloud and enabling the integration of open source tools for spatial ‘omics analytics
Authors: Jason W. Reeves, David Henderson, Matt Crow, April Munn, Kenlyn Terai, Joachim Schmid
Journal: Cancer Research (2023)

Abstract Spatial biology is revolutionizing the way in which we extract biological insights from precious clinical samples, allowing profiling of thousands of RNA species and ever higher numbers of antibodies to be analyzed from a single tissue slide. But with new 'omics capabilities scaling the analytical and infrastructure requirements for these high-content datasets is more critical than ever, as these datasets contain billions of data points and hundreds of images that require more extensive storage and analysis capabilities. To enable scientists to leverage spatial 'omics instruments, we have launched the AtoMx™ Spatial Informatics Platform, which will enable analytics across NanoString's spatial profiling and imaging solutions.The AtoMx platform was designed to specifically host, ingest, and manage data generated from both the GeoMx® Digital Spatial Profiler and the CosMx™ Spatial Molecular Imager. Data generated by either of these platforms is analyzed, stored, and managed in cloud or private HPC environments. Within the AtoMx platform, we provide native, comprehensive analysis suites specifically designed to integrate the high content, multiplexed imaging from either platform with the molecular readouts. Machine learning methods in key analysis modules allow AtoMx to scale to the billions of data points collected while still maintaining lower compute times. The AtoMx platform is built to conform to open data standards and will support customization through custom analysis scripts, APIs for integration to external software, and a community standard data model that facilitates the integration of tools in open source repositories.With the CosMx platform we have been able to demonstrate a 75x decrease in data processing times compared to locally resourced servers for equivalent data analysis requests by utilizing the scaling tools a cloud service provides such as scaling by compute type for greater RAM access or multiple, parallel compute instances. The platform is designed to facilitate data sharing and collaborative in silico analysis of spatial data, with direct permissions management and compliance with regional privacy requirements. The AtoMx Spatial Informatics Platform provides an extensible, secure management and analysis solution, capable of processing transcriptome-wide expression or high plex protein profiling from the GeoMx Digital Spatial Profiler as well as subcellular spatial 'omics data Citation Format: Jason W. Reeves, David Henderson, Matt Crow, April Munn, Kenlyn Terai, Joachim Schmid. Solving the problem of spatial informatics: Harnessing the power of the cloud and enabling the integration of open source tools for spatial ‘omics analytics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2083.